CropGF

CropGF enables mining and analysis of gene families across rice, wheat, maize, barley, sorghum, foxtail millet, and Arabidopsis thaliana to support comparative genomics and functional inference.

Key Features:

• Extensive Gene Database: Contains 314,611 genes across six major crops (rice, wheat, maize, barley, sorghum, foxtail millet) and the model organism Arabidopsis thaliana.
• Domain Coverage: Catalogs 4,399 domain types to represent structural and functional diversity within gene families.
• Versatile Search System: Supports keyword queries and BLAST-based homology searches to identify gene families and member genes by domain or sequence homology.
• Integrated Data Sources: Integrates corresponding ID information from various public databases for both genes and domains.
• Downstream Analysis Modules: Implements ka/ks ratio analysis, phylogenetic tree construction, and subcellular localization analysis.
• Multi-omics Data Support: Leverages genomics, transcriptomics, and proteomics data for holistic gene family characterization.
• Visualization: Produces visual outputs to interpret genetic relationships and functional annotations across species.

Scientific Applications:

• Comparative Genomics: Enables cross-species comparison of gene family composition and evolution among major crops and Arabidopsis thaliana.
• Functional Inference: Supports identification of candidate genes for trait-related functions via domain, homology, and ka/ks analyses.
• Breeding and Trait Research: Facilitates selection of candidate genes for crop improvement and investigation of molecular bases of plant adaptation.
• Phylogenetics and Molecular Evolution: Supports phylogenetic analyses to study gene family expansion and evolutionary relationships.

Methodology:

Performs keyword and BLAST-based homology searches, integrates genomics, transcriptomics, and proteomics datasets with public-database IDs, and applies ka/ks ratio calculations, phylogenetic tree construction, and subcellular localization analysis.